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<p>Namespace for dynamic programming classes.  
<a href="#details">More...</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmoltk_1_1dp_1_1GapScore.html">GapScore</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Parameters for scoring indel gaps in sequence alignments.  <a href="structmoltk_1_1dp_1_1GapScore.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmoltk_1_1dp_1_1GapScore_3_01SCORE__TYPE_00_011_01_4.html">GapScore&lt; SCORE_TYPE, 1 &gt;</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">template specialization for affine gap score function  <a href="structmoltk_1_1dp_1_1GapScore_3_01SCORE__TYPE_00_011_01_4.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__GAPPED__ALIGNMENTS_00_01GAP__NSEGS_01_4.html">DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_GAPPED_ALIGNMENTS, GAP_NSEGS &gt;</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Specialization of alignment column cache for alignment of alignments.  <a href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__GAPPED__ALIGNMENTS_00_01GAP__NSEGS_01_4.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__UNGAPPED__SEQUENCES_00_01GAP__NSEGS_01_4.html">DPPosition&lt; SCORE_TYPE, dp::DP_ALIGN_UNGAPPED_SEQUENCES, GAP_NSEGS &gt;</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Specialization of alignment column cache for alignment two individual sequences.  <a href="structmoltk_1_1dp_1_1DPPosition_3_01SCORE__TYPE_00_01dp_1_1DP__ALIGN__UNGAPPED__SEQUENCES_00_01GAP__NSEGS_01_4.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmoltk_1_1dp_1_1RunningScore.html">RunningScore</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Generic accumulated score in a <a class="el" href="structmoltk_1_1dp_1_1DPCell.html" title="Generic node in dynamic programming table.">DPCell</a>.  <a href="structmoltk_1_1dp_1_1RunningScore.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmoltk_1_1dp_1_1RunningGapScore_3_01SCORE__TYPE_00_01DP__ALIGN__UNGAPPED__SEQUENCES_00_011_01_4.html">RunningGapScore&lt; SCORE_TYPE, DP_ALIGN_UNGAPPED_SEQUENCES, 1 &gt;</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Template specialization for single sequence affine gap running score (E or F in Gusfield recurrence)  <a href="structmoltk_1_1dp_1_1RunningGapScore_3_01SCORE__TYPE_00_01DP__ALIGN__UNGAPPED__SEQUENCES_00_011_01_4.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmoltk_1_1dp_1_1RunningGapScore_3_01SCORE__TYPE_00_01DP__ALIGN__GAPPED__ALIGNMENTS_00_011_01_4.html">RunningGapScore&lt; SCORE_TYPE, DP_ALIGN_GAPPED_ALIGNMENTS, 1 &gt;</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Template specialization for alignment of alignments affine gap running score (E or F in Gusfield recurrence)  <a href="structmoltk_1_1dp_1_1RunningGapScore_3_01SCORE__TYPE_00_01DP__ALIGN__GAPPED__ALIGNMENTS_00_011_01_4.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmoltk_1_1dp_1_1DPCell.html">DPCell</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Generic node in dynamic programming table.  <a href="structmoltk_1_1dp_1_1DPCell.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmoltk_1_1dp_1_1AlignmentResult.html">AlignmentResult</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Gap structure and score of a pairwise sequence alignment, used as an intermediate value during sequence alignment.  <a href="structmoltk_1_1dp_1_1AlignmentResult.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structmoltk_1_1dp_1_1DPTable_3_01SCORE__TYPE_00_01DP__MEMORY__LARGE_00_01ALIGN__TYPE_00_011_01_4.html">DPTable&lt; SCORE_TYPE, DP_MEMORY_LARGE, ALIGN_TYPE, 1 &gt;</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">template specialization of DPTable for Affine alignment in large memory.  <a href="structmoltk_1_1dp_1_1DPTable_3_01SCORE__TYPE_00_01DP__MEMORY__LARGE_00_01ALIGN__TYPE_00_011_01_4.html#details">More...</a><br/></td></tr>
<tr><td colspan="2"><h2><a name="enum-members"></a>
Enumerations</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647fe">DPMemoryModel</a> { <a class="el" href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647feab8548c282fd21547171c41cb000859b2">DP_MEMORY_LARGE</a>, 
<a class="el" href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647fea55075aaaa2895a6d9dd46271a9ca0ab3">DP_MEMORY_SMALL</a>
 }</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Fast O(n^2) memory use vs. 2X slower O(n) memory use.  <a href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647fe">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8a">DPAlignGapping</a> { <a class="el" href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8aa19b182379f9aee058d724619e502727c">DP_ALIGN_UNGAPPED_SEQUENCES</a>, 
<a class="el" href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8aad39f6552ff8d735f2b69a72f560d8c90">DP_ALIGN_GAPPED_ALIGNMENTS</a>
 }</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Whether alignment operands have preexisting gaps (e.g. alignments) or not (e.g. single sequences)  <a href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8a">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4">DPAlignScale</a> { <a class="el" href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4af155cf0d0612b514f7738fa8de8735ce">DP_ALIGN_GLOBAL</a>, 
<a class="el" href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4a42868d0ce46f2b0c694131013b187e0d">DP_ALIGN_LOCAL</a>
 }</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Global vs. local alignment.  <a href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0c">TracebackPointer</a> { <a class="el" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0ca9d2fbcded45ce4a53f3dfc4d93ae9f42">TRACEBACK_UPLEFT</a>, 
<a class="el" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0cab17ffddcd5713d8a8d67ebfcff4fccdc">TRACEBACK_UP</a>, 
<a class="el" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0ca448324d993ba9dd1c87753515d34d6ee">TRACEBACK_LEFT</a>
 }</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">TracebackPointer to help reconstruct the final alignment.  <a href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0c">More...</a><br/></td></tr>
<tr><td colspan="2"><h2><a name="func-members"></a>
Functions</h2></td></tr>
<tr><td class="memTemplParams" colspan="2">template&lt;typename SCORE_TYPE , DPMemoryModel MEMORY_MODEL, DPAlignGapping ALIGN_TYPE, int GAP_NSEGS&gt; </td></tr>
<tr><td class="memTemplItemLeft" align="right" valign="top">std::ostream &amp;&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="namespacemoltk_1_1dp.html#a77b7e3ce0c9cfe4b90734b8466b1c782">operator&lt;&lt;</a> (std::ostream &amp;os, const moltk::dp::DPTable&lt; SCORE_TYPE, MEMORY_MODEL, ALIGN_TYPE, GAP_NSEGS &gt; &amp;t)</td></tr>
<tr><td class="memTemplParams" colspan="2">template&lt;typename SCORE_TYPE , DPAlignGapping ALIGN_TYPE, int GAP_NSEGS&gt; </td></tr>
<tr><td class="memTemplItemLeft" align="right" valign="top">std::ostream &amp;&#160;</td><td class="memTemplItemRight" valign="bottom"><a class="el" href="namespacemoltk_1_1dp.html#a33dc6de12eb00df778f3c9694269c3a5">operator&lt;&lt;</a> (std::ostream &amp;os, const std::vector&lt; std::vector&lt; <a class="el" href="structmoltk_1_1dp_1_1DPCell.html">moltk::dp::DPCell</a>&lt; SCORE_TYPE, ALIGN_TYPE, GAP_NSEGS &gt; &gt; &gt; &amp;)</td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Namespace for dynamic programming classes. </p>
<p>Many of theses classes use hard-to-read C++ template specializations, because we are trying to avoid the overhead of virtual functions and and branching logic in the time-critical inner loop of dynamic programming. </p>
</div><hr/><h2>Enumeration Type Documentation</h2>
<a class="anchor" id="ae2384a91af43f1f96d02fa69319a0a8a"></a><!-- doxytag: member="moltk::dp::DPAlignGapping" ref="ae2384a91af43f1f96d02fa69319a0a8a" args="" -->
<div class="memitem">
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      <table class="memname">
        <tr>
          <td class="memname">enum <a class="el" href="namespacemoltk_1_1dp.html#ae2384a91af43f1f96d02fa69319a0a8a">moltk::dp::DPAlignGapping</a></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Whether alignment operands have preexisting gaps (e.g. alignments) or not (e.g. single sequences) </p>
<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em><a class="anchor" id="ae2384a91af43f1f96d02fa69319a0a8aa19b182379f9aee058d724619e502727c"></a><!-- doxytag: member="DP_ALIGN_UNGAPPED_SEQUENCES" ref="ae2384a91af43f1f96d02fa69319a0a8aa19b182379f9aee058d724619e502727c" args="" -->DP_ALIGN_UNGAPPED_SEQUENCES</em>&nbsp;</td><td>
<p>Alignment with no preexisting gaps can be faster and truly optimal. </p>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="ae2384a91af43f1f96d02fa69319a0a8aad39f6552ff8d735f2b69a72f560d8c90"></a><!-- doxytag: member="DP_ALIGN_GAPPED_ALIGNMENTS" ref="ae2384a91af43f1f96d02fa69319a0a8aad39f6552ff8d735f2b69a72f560d8c90" args="" -->DP_ALIGN_GAPPED_ALIGNMENTS</em>&nbsp;</td><td>
<p>Alignment of pregapped sequences is slower and heuristic (problem is NP-hard) </p>
</td></tr>
</table>
</dd>
</dl>

</div>
</div>
<a class="anchor" id="aa392b3f92a66c78410a845eb35e069b4"></a><!-- doxytag: member="moltk::dp::DPAlignScale" ref="aa392b3f92a66c78410a845eb35e069b4" args="" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">enum <a class="el" href="namespacemoltk_1_1dp.html#aa392b3f92a66c78410a845eb35e069b4">moltk::dp::DPAlignScale</a></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Global vs. local alignment. </p>
<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em><a class="anchor" id="aa392b3f92a66c78410a845eb35e069b4af155cf0d0612b514f7738fa8de8735ce"></a><!-- doxytag: member="DP_ALIGN_GLOBAL" ref="aa392b3f92a66c78410a845eb35e069b4af155cf0d0612b514f7738fa8de8735ce" args="" -->DP_ALIGN_GLOBAL</em>&nbsp;</td><td>
<p>Global alignment (Needleman Wunsch) </p>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="aa392b3f92a66c78410a845eb35e069b4a42868d0ce46f2b0c694131013b187e0d"></a><!-- doxytag: member="DP_ALIGN_LOCAL" ref="aa392b3f92a66c78410a845eb35e069b4a42868d0ce46f2b0c694131013b187e0d" args="" -->DP_ALIGN_LOCAL</em>&nbsp;</td><td>
<p>Local alignment (Smith Waterman) </p>
</td></tr>
</table>
</dd>
</dl>

</div>
</div>
<a class="anchor" id="a3847dc6be50dae17fff97f2d922647fe"></a><!-- doxytag: member="moltk::dp::DPMemoryModel" ref="a3847dc6be50dae17fff97f2d922647fe" args="" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">enum <a class="el" href="namespacemoltk_1_1dp.html#a3847dc6be50dae17fff97f2d922647fe">moltk::dp::DPMemoryModel</a></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Fast O(n^2) memory use vs. 2X slower O(n) memory use. </p>
<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em><a class="anchor" id="a3847dc6be50dae17fff97f2d922647feab8548c282fd21547171c41cb000859b2"></a><!-- doxytag: member="DP_MEMORY_LARGE" ref="a3847dc6be50dae17fff97f2d922647feab8548c282fd21547171c41cb000859b2" args="" -->DP_MEMORY_LARGE</em>&nbsp;</td><td>
<p>Faster O(n^2) memory model. </p>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="a3847dc6be50dae17fff97f2d922647fea55075aaaa2895a6d9dd46271a9ca0ab3"></a><!-- doxytag: member="DP_MEMORY_SMALL" ref="a3847dc6be50dae17fff97f2d922647fea55075aaaa2895a6d9dd46271a9ca0ab3" args="" -->DP_MEMORY_SMALL</em>&nbsp;</td><td>
<p>2X slower O(n) memory model </p>
</td></tr>
</table>
</dd>
</dl>

</div>
</div>
<a class="anchor" id="acda879cd7560136dfc3f46cf568aff0c"></a><!-- doxytag: member="moltk::dp::TracebackPointer" ref="acda879cd7560136dfc3f46cf568aff0c" args="" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">enum <a class="el" href="namespacemoltk_1_1dp.html#acda879cd7560136dfc3f46cf568aff0c">moltk::dp::TracebackPointer</a></td>
        </tr>
      </table>
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<div class="memdoc">

<p>TracebackPointer to help reconstruct the final alignment. </p>
<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em><a class="anchor" id="acda879cd7560136dfc3f46cf568aff0ca9d2fbcded45ce4a53f3dfc4d93ae9f42"></a><!-- doxytag: member="TRACEBACK_UPLEFT" ref="acda879cd7560136dfc3f46cf568aff0ca9d2fbcded45ce4a53f3dfc4d93ae9f42" args="" -->TRACEBACK_UPLEFT</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="acda879cd7560136dfc3f46cf568aff0cab17ffddcd5713d8a8d67ebfcff4fccdc"></a><!-- doxytag: member="TRACEBACK_UP" ref="acda879cd7560136dfc3f46cf568aff0cab17ffddcd5713d8a8d67ebfcff4fccdc" args="" -->TRACEBACK_UP</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="acda879cd7560136dfc3f46cf568aff0ca448324d993ba9dd1c87753515d34d6ee"></a><!-- doxytag: member="TRACEBACK_LEFT" ref="acda879cd7560136dfc3f46cf568aff0ca448324d993ba9dd1c87753515d34d6ee" args="" -->TRACEBACK_LEFT</em>&nbsp;</td><td>
</td></tr>
</table>
</dd>
</dl>

</div>
</div>
<hr/><h2>Function Documentation</h2>
<a class="anchor" id="a77b7e3ce0c9cfe4b90734b8466b1c782"></a><!-- doxytag: member="moltk::dp::operator&lt;&lt;" ref="a77b7e3ce0c9cfe4b90734b8466b1c782" args="(std::ostream &amp;os, const moltk::dp::DPTable&lt; SCORE_TYPE, MEMORY_MODEL, ALIGN_TYPE, GAP_NSEGS &gt; &amp;t)" -->
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template&lt;typename SCORE_TYPE , DPMemoryModel MEMORY_MODEL, DPAlignGapping ALIGN_TYPE, int GAP_NSEGS&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">std::ostream&amp; moltk::dp::operator&lt;&lt; </td>
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          <td class="paramtype">const moltk::dp::DPTable&lt; SCORE_TYPE, MEMORY_MODEL, ALIGN_TYPE, GAP_NSEGS &gt; &amp;&#160;</td>
          <td class="paramname"><em>t</em>&#160;</td>
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          <td>)</td>
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<a class="anchor" id="a33dc6de12eb00df778f3c9694269c3a5"></a><!-- doxytag: member="moltk::dp::operator&lt;&lt;" ref="a33dc6de12eb00df778f3c9694269c3a5" args="(std::ostream &amp;os, const std::vector&lt; std::vector&lt; moltk::dp::DPCell&lt; SCORE_TYPE, ALIGN_TYPE, GAP_NSEGS &gt; &gt; &gt; &amp;)" -->
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<div class="memproto">
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template&lt;typename SCORE_TYPE , DPAlignGapping ALIGN_TYPE, int GAP_NSEGS&gt; </div>
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          <td class="memname">std::ostream&amp; moltk::dp::operator&lt;&lt; </td>
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          <td class="paramtype">const std::vector&lt; std::vector&lt; <a class="el" href="structmoltk_1_1dp_1_1DPCell.html">moltk::dp::DPCell</a>&lt; SCORE_TYPE, ALIGN_TYPE, GAP_NSEGS &gt; &gt; &gt; &amp;&#160;</td>
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